docs: def _align_sequences_to_hmm(self, hmm_file, sequences_file, output_alignment_file):
          '''Align sequences to an HMM, and write an alignment of
          these proteins after cleanup so that they can be used for tree-making
  
          Parameters
          ----------
          sequences_file: str
              path to file of unaligned protein sequences
          hmm_file: str
              path to hmm file
          output_alignment_file: str
              write alignment to this file
  
          Returns
          -------
          nothing
          '''
  
          ss = SequenceSearcher(hmm_file)
          with tempfile.NamedTemporaryFile(prefix='graftm', suffix='.aln.fasta') as tempalign:
              ss.hmmalign_sequences(hmm_file, sequences_file, tempalign.name)
              ss.alignment_correcter([tempalign.name], output_alignment_file)